Pokémon World at War
by Gardevoir91
Summary: This is a story that I have been dying to publish somewhere. I am a rough-around-the-edges kind of writer, but I do hope you'll enjoy it. I'm new to the site, and I am so excited to get this story/party started! XD (Caution! May contain strong language at times, along with some lemons.)
1. Prologue

**Pokémon World at War**

**Disclaimer: I do not own Pokémon. **

**Prologue: **Pokéhumans, Pokéblood, Pokémorph...all of these terms are used to describe something, or someone. That someone/individual is said to be a mediator between humans and Pokémon so the two may live in harmony. There are the original types: Fire, grass, water, psychic, dark, fighting, flying, electric, steel, ice, poison, ground, rock, bug, and dragon. There are several individuals of each type within the entire world...even including the new fairy type. However...there is one Pokéhuman who has all of these traits. This individual is known as the Universal Pokéhuman, or Universal for short.

They choose to live their lives as normally as possible to keep the legend safe; For if someone finds out, who knows what will come of it.


	2. Chapter 1: It was only a dream

**Pokémon World at War 1**

**Chapter 1: It was only a dream...sigh**

_A young girl just turned ten years old. Her father, a Ranger woke her up, his face alight about something. He also went into her mother and father's room to wake up his wife. They could smell he was covered in soot, and his hair wasn't the usual blonde color it is...such is the life he chose. He ushered his two most treasured girls outside to watch an araura borealis right in front of their eyes. He wraps them both tightly one in each arm and sighs in excitement. "Isn't this wonderful?" He looks at them both, his head turning left to right the whole time. His wife nods, along with their daughter. He kneels down and looks at his daughter straight in her eyes. "And just think...in only a matter of eight hours from now, you'll become a trainer!" The woman giggles. "Oh Aaron..." He looks at her confusedly. "What is it, Susan?" "Watching you getting all fired up over our Sierra becoming a trainer." _

**/**

The dream continues as she sleeps with tears in her eyes about her family. _Aaron wakes them all up once again at ten to eight in the morning to get Sierra up and going. They get her Pokémon license and she chooses her first Pokémon, Cyndaquil. "Wonderful choice, Sierra." Says Professor Elm. "You may nickname him if you like. She studies her newfound friend and then says "Your name will be...Blaizer!" Her father chuckles. "Aaron!" Scolds Susan. "I'm sorry. That's usually a catch phrase of mine for when a fire is really nasty. That's all." _

_After a few more words are said, Professor Elm gets them in a family portrait and Sierra wakes up to a flash of light._

"Wake up squirt! We got orders from da boss that we gotta do." She was woken up to the flash of the light in her quarters that she was sharing with one of the higher ups of Team Rocket. She sighs and wipes the tears from her eyes. _'Another day in paradise I suppose.' _She thinks to herself as she gets into the cursed uniform for she can't remember how long.


	3. Chapter 2: SS Anne Heist

**Pokémon World At War 2**

**Chapter 2: S.S. Anne Heist**

Sierra sighs and puts on her uniform as she listens to the higher up bark at her. She just looks at her with an apathetic look and continues getting ready. "And on top of that...he wants you to wear this." The Rocket pulls out a uniform that looks like it will fit her...except one thing: Sierra hates anything that leaves her legs bare and open, so skirts and dresses fit that category of hers to a "T". She looks at the Rocket and gives her a glare. The Rocket flinches, and leaves it on the door hanging in front of her. "I'll let the boss know you're changing. We got a big day today." Sierra nods and changes into the red uniform that has the accursed skirt she so much 'loves' to wear. She walks out to the van where some of the other Rocket members are waiting for her and they all get to their destination: The S.S. Anne.

Sierra's only heard of it, but to see it up close...she can't imagine what's inside it.

They get inside and into position. She sees her second cousin, James, along with Jessie and Meowth. She can't help but snicker as James gets suckered into buying the Magikarp...but...she does care about him...mainly because he is family.

Almost everything goes without a single hitch until the machine shows up and starts sucking everything in its path. Sierra, already skilled with the stolen Pokémon she was given, a Houndoom, knocked out at least two challengers on her own before things got really hairy.

The ship starts to go down and she gets on one of the rescue boats, hoping that James and Co. would soon follow...but to no avail. They decide to chase after "the twerps".

**/**

After everything was said and done, they all return to headquarters, and she overheard some of the executives about giving some of the Rockets, mainly the trio that always fails, some major punnishment. Sierra goes into Giovanni's office without permission to speak with him personally. He turns around in his chair, the Persian under his hand enjoying the petting it was getting from its master.

"What is it, Sierra?" Giovanni growls. She clears her throat to gain courage. "I wish to speak to you about Jessie, James, and Meowth sir. It was not entirely their fault for what happened to the S.S. Anne." He smirks. "Is that so?" Sierra nods. "I believe so, yes. If there is going to be any punnishment, don't harm them. They already get enough trouble from the Pikachu they're trying to capture." He tilts his head. "Then who should I deal punnishment?" He cocks an eyebrow.

She swallows hard out of nerves. "Me." He leans back in his chair almost out of shock. He calls Professor Namba and has him arrange something, then Sierra is dragged off to the lab...surprisingly, without a fight.

There were two tables, and there was clear tubing connected to each of them. On one table, a Ditto was being held captive, and Sierra was dragged into the other one and strapped down nice and tight. "Aww...don't struggle little girl. It might just rile _us_ up." Says one of the grunts. "Make sure she's secured tightly now. This...experiment is going to commence!" They start up the machine and the Ditto, as it was near death as it was, was being sucked away in and through the tubes...and Sierra watched in horror as the pink liquid that was the Ditto was being infused into Sierra. She tears up, watching how the Ditto was suffering and tries to struggle, but to no avail...the bonds were too tight for her to do anything. Within half an hour, the Ditto was gone, and Sierra blacks out.


	4. Chapter 3: Powers Awakened!

**Pokémon World at War **

**Chapter 3: Powers Awakened!**

After about three days being blacked out, Sierra finds herself in the Team Rocket Headquarters infermery. How she got there, she doesn't know. She looks around to see if anyone was there, and she decides to get up and walk around a bit. She goes passed a mirror, then backtracks to it to look at her reflection, and almost panics. Her hair wasn't the deep blue as it once was...but...more of a pink color. Somewhere between Ditto...and maybe Mew? Perhaps?

Seeing this new change isn't exactly welcoming to her. She misses her blue hair already. Wait...there's something else as well. '_Oh no! Did I black out? For how long? My beautiful hair...mother's gonna flip! Not to mention...'_ She tears up a little. _'Dad is probably rolling in his grave because of where I am now. Huh?_' She turns her head to see a note saying:

_Sierra,_

_When you get this message, I have something...or rather...someone to show you. Perhaps you can teach him things that I cannot._

_Giovanni_

Her mind is blown reading this kind of message. She straightens her hair, gets into a clean uniform, and runs for his office...but without bumping into anyone like she normally would. Everything about her seemed...off. Not in a bad way...but...she doesn't know if it's good either.

She knocks on his door and he greets her at the door. "Come with me."

She nods and follows him to a part of the building she's only seen once, through that part, and into the arena. He opens a gate at the press of a button to reveal a Pokémon that they have been cloning for what seemed like decades.

"Mewtwo, I would like you to meet someone. She has a knack for battling, and perhaps she's the one you're looking for." Sierra looks in awe as Giovanni takes a seat and Mewtwo begins walking towards her.

"Yes. You are the One." Sierra's taken aback at his immense psychic energies. "The one what? If I may ask?" Mewtwo seemed to chuckle at her naivity a bit. "Can you not sense the power you possess?" She takes a step back from him. _'This pressure...is it his ability? I feel like I'm being pushed down.'_ She thinks to herself. "Yes. This is my ability." Sierra looks up at Giovanni with a worried look on her face and then looks back at Mewtwo, trying to gain her composure. "I have noticed I've been feeling different, but I don't really know what it is. I was blacked out for three days." "And within those three days, your powers have awakened. Your hair color is now almost the same as Mew's. That tells me something." Sierra nods in agreement.

**/**

They chat for what seems like hours. Giovanni actually up and left without their knowing. A sign of trust, perhaps? Sierra smiles at her newfound friend. "I have been wondering. What do you think about a being such as I?" Sierra looks at Mewtwo a little awestruck. "What do _I_ think? Well...For starters, just because you are an artificial Pokémon, doesn't make you any less alive than a naturally born one. I find you no less important than any other Pokémon on this planet. You are here for a purpose. I am not sure myself on what your purpose is, but I'm sure it will come to be known to you." Now it's Mewtwo's turn to awestruck. Here's an individual who sounds like she cares about almost anything and everything that lived. He nods, and it almost seems like he smiles. With a couple more exchanged words, they part and Mewtwo goes back to where he is being contained for the time being.

**/**

Two years after that encounter, Sierra turns 13. Giovanni gave her his word that if she were to escape without using her powers that she would be free from her servitude of Team Rocket. Bound and determined, she sets out. _'Well...so far...so good. Almost outside too!'_ She thinks to herself as she sneaks through the building late at night, but close to dawn. Scared of being caught too soon, she jumps out a window and starts running through a field. Giovanni sits in his chair watching the whole thing. She looks down at the Pokéball containing her partner from Newbark Town and kisses it as she runs.

Giovanni's peace and quiet, and his amusement is interrupted abruptly by a grunt. "Sir! What should we do? She escaped!" He sighs and looks at the grunt with an irritated expression on his visage. "Leave her be. She escaped. I will keep my word." He tosses a purple ball at the grunt. The purple ball that is sought after by many collectors: the Master Ball. The grunt looks at him confused. "Give that to her. It's hers." Giovanni says in a lighter tone. The grunt salutes and goes off to deliver the item to her. After doing so, Sierra puts the ball in her pack and teleports back to Newbark. "Mom?! I'm home!" She says with tears in her eyes. The sight of home could be no sweeter than what it was right then.

* * *

**(Woohoo! Three chapters in two days! This is so totally awesome. Thank you for subscribing and/or just viewing the story, and I will try my best to keep each of the chapters uploaded as regularly as possible. Please do not be shy about leaving any comments below. Maybe some constructive criticism please, as I am new to the site yet. I don't know about you all, but I am having a blast!)**


	5. Chapter 4: Not Guilty?

**Pokémon World at War**

**Chapter 4: Not guilty?**

Sierra realizes that she just teleported home and is unable to think about it as she had something she needed to do before she could think of anything. She goes upstairs to her room to realize that none of her clothes fit her anymore, and she sighs. "So much for that idea, huh Blaizer?" "Quil..." The Cyndaquil gives her a little glare. He hated the idea of his master being in such an evil organization, and he almost hated her for it, too. She kneels down and starts to try to talk to him, but to no avail. "Oh...alright. Be that way. You have got to be one of the most stubborn Pokémon I've ever met." She didn't say it in a mean tone of voice at all though...rather...in a friendly tone. "Tell you what...how about you can follow me around for a little bit, huh?" The Cyndaquil tilts her head in curiosity. "Quil?" "Yeah. I'll let you roam off, but you have to come back. Okay?" The Cyndaquil just nods his head and they walk out of the house and all the way to Goldenrod City where her mother works. Before they could do that, they hear sirens from afar. "Quil?" Sierra looks at her Cyndaquil and gives him a confident look. "It's okay, Blaizer. They're probably in the middle of an eme-" Before she could get the rest of her sentence out, they're surrounded. Her Cyndaquil as if even out of instinct starts flaring up his back. "Blaizer! It's okay. They won't hurt us." He stops flaring up and she calls him back to his Pokéball. She puts her hands up and the officers take them to Goldenrod City for a hearing.

Sierra sighs. She knew this was coming. The judge looks at her with a stern look. "Do you, Sierra Phoenix swear to tell the truth, the whole truth, and nothing but the truth?" She keeps her right hand up. "I do." The judge nods. "Very well. Please...tell us why you have chosen this path of being a criminal." Sierra takes a hard gulp. She didn't know if her being honest was actually going to be made fun of. She takes a deep breath, and begins.

"To be truthfully honest, Your Honor, I was kidnapped into Team Rocket but only hours after I was supposed to start my journey. My Cyndaquil, Blaizer...he was chosen by me to be my partner. I wanted to do everything to keep him safe by doing everything they told me to do. To tell you the truth sir, I almost do not deserve to be a trainer at this point. I didn't want him hurt. I don't care what happens to me as long as they did no harm to my Blaizer, your Honor. It sounds ridiculous, it sounds prepostorous, it sounds highly unlikely, but yes...I was a criminal, and I will do the time. If necessary, give Blaizer back to Professor Elm. He's safe..and that's all that matters to me."

A woman dressed in an officer's uniform stands up, almost in disbelief in what she has heard. "Your Honor, if I may say something..."

"Overruled!" The judge silences her. "We will discuss your disciplinary actions as we take a brief intermission."

Sierra nods and the case is dismissed for an hour. When they come back, they have their answer.

They say a few more words back and forth until finally, the Judge asks the Jury what they find.

"We the Jury find the defendant...Not Guilty."

Sierra slumps back in her chair in disbelief. She is humbled to find that she is innocent of all of her crimes.

The same officer that tried to put in her two cents goes up to Sierra and hugs her.

"I'm so relieved, hon." She tightens her grip around her mother, Officer Susan. "I..I am too, mom."

"Looks like we need to do some clothes shopping for you, huh?" Her mother's tone perks up a bit.

"Yeah...we do." Sierra chuckles.

"I do have to ask...what happened to your hair?"

"That's a long story, mom. Maybe after we go shopping?"

"Sure thing dear."

_'Arceus it's good to be home!'_ She thought to herself as they head out of the court room and to a clothing store.

* * *

**(Woo! Hi guys. Sorry it's been a while. I've been busy with some things. But anyways, here's the new chapter. And it seems like I might need to explain my story a little bit...There's going to be two peaks. The first one is the beginning of the war, the second is the last battle of the war, and of course the ending. In case you are wondering, that is what's going to happen. There will be time jumps, so don't panic. I will have the more major events happen either in flashbacks, or I might actually have them happen throughout the story. It depends.)**


	6. Chapter 5: Starting Anew

**Pokémon World at War**

**Chapter 5: To Start Anew**

After they get done with shopping, they get home and Sierra replaces her old clothing with her new. They sit down on the couch and Sierra explains what happens, ending up in tears. Her mother, shocked at what she has just heard come from her now 13-year-old daughter, she wraps her arms around her and holds her tight.

"I can't believe that they could do something like that. You are very brave for doing that kind of thing, Sierra. Don't let anyone tell you otherwise. Alright?"

Sierra nods and wipes her tears away. "Yeah."

Susan rubs her back for a little while and goes to start warming up some water for tea over the stove. Sierra brings out her Cyndaquil and he starts wandering around the house, curious about his surroundings. "Don't go burning anything down now, okay?" Sierra tells him in a slightly serious tone of voice. The Cyndaquil nods and walks up behind Susan and starts rubbing his head against her leg. Susan giggles. "Well aren't you a cutie? Glad to see you're okay."

Blaizer looks up at her with a smile. "Quil!" Susan chuckles a bit and continues with something in the kitchen...until an Ariados pops up out of the closet. "Aria...Ariados."

Sierra watches her Cyndaquil very carefully as he approaches her deceased father's Ariados. It starts out kind of sketchy, but it slowly gets to be a more friendly and inticing conversation. The Ariados explains how it got into the house, and Cyndaquil does the same, then Susan jumps slightly at seeing the bug Pokémon hanging in the closet.

"Webbie, how many times have I asked you not to do that?"

The Ariados saddens a little, remembering that her master, Aaron thought it was funny. Sierra begins to chuckle which cheered her up a bit. "Oh mom...she used to play that trick on you since she was a Spinarak." The Ariados really starts smiling, and Susan starts to tear up a bit, remembering how much she really misses Aaron. Sierra sighs and goes up to her and gives her a hug.

"I'm sorry mom. I miss him too." She hugs her mother tightly to help her calm down.

Once her mother gains her composure again, the Ariados walks up to Susan and does the same thing Blaizer did moments before.

Susan looks at the Ariados with a sad smile and kneels to pet her. "I'm sorry. I know your master liked it when you played that trick, but it still startles me sometimes." The Ariados nods understandingly. "Ariados."

The Ariados starts looking at the door almost with a panic. "Ariados..Ar...Aria."

Sierra rushes to open the door, ready to take on the trouble to see that a thunderstorm was on the way. Seeing no real danger, she turns to the unnereved Ariados, remembering that she doesn't like storms. She kneels down and pets the Ariados as well. "Don't worry. We're all safe, dry, and warm in here. Okay?"

The Ariados, aka Webbie, nods nervously.

"Dinner's ready!" Hollers Susan, and everyone gathers around the table, including the Pokémon.

"Ah, ah ah. You know the rules, Webbie." Webbie chuckles and gets down onto all of her legs from leaning up on the chair. Susan lays down a bowl of Pokémon food for her, and for Blaizer as well.

Susan lets out a happy sigh. "There. Now that they're happy, let's dig into our own food." Sierra nods in agreement and they dig in as the storm moves through.

**/**

The next day at around 4 a.m., Susan starts her day and goes off to work, leaving a note for Sierra about her going to Goldenrod City. She hates that she can't be with her daughter to catch up on lost time, but duty calls. She puts her cap on, grabs her gear, and heads out on her bike to Goldenrod. She likes the early shifts. Work longer hours, and get off the clock earlier in the day as well. It takes her about an hour to get ready and head to her job, but she can't complain. Not when she goes through a beautiful forest, and a cave.

Meanwhile, Sierra wakes up and gets dressed, and begins to prepare to actually set off on her journey like she should have 3 years ago. She gently wakes up her Cyndaquil.

"Come on Blaizer...time to wake up." He just lays there, still sleeping. Sierra smiles and decides to clean up the house a bit until he actually wakes up and climbs down the stairs, along with Webbie.

She looks at the two and smiles as she just finishes sweeping the floors. "Well...glad to see the two of you are awake." "Quil! Cyndaquil!" "Ariados!"

Sierra smiles and gives them breakfast before feeding herself.

"Hey Blaizer? I have a question for you."

He tilts his head at her curiously. "Quil?"

"I know you don't like me and all...but...we are partners, and I was wondering if we could travel together like we were supposed to about three years ago?" She begins to tear up.

"The reason I say this is because...I did all of those nasty things in Team Rocket because I didn't want you to get hurt. I know it was wrong. I did it because I wanted to protect you, and because I didn't know if they were going to actually hurt you if I didn't obey."

Blaizer looks at her and he begins to tear up some. Sierra slowly puts her hands and arms around him and they cuddle for a little while before they head out. Sierra looks at Webbie after a while.

"Hey Webbie, do you want to come with me as well, or would you rather stay here."

"Ariados."

Sierra nods. Hearing that Webbie would rather stay home didn't bother her any.

"Okay. Take care of things while we're gone."

Sierra writes a note and leaves it on the table for her mother so she knows where her daughter is...or isn't, grabs a new backpack that was labeled "_For Sierra_", along with a new Pokégear and heads out.

Days pass and they make their way to Violet City after training for a long time. She makes her way to the Sprout Tower to train some more, and to catch a Bell Sprout. After doing so, she goes back to the house where a man was wanting to trade a Bellsprout for an Onix named Rocky.

Sierra felt bad about trading her Bellsprout, but she was going to need the type advantage against Falkner, the Gym Leader.

**/**

After training for another day or so, Sierra gathered up a team consisting of a Sentret, Cyndaquil, Onix, and Pidgey. She stands in front of the gym doors and takes a breath before entering.

"Welcome to the Violet City Gym. I am Falkner."

Sierra smiles. "Hello Falkner. I am here to challenge you."

"Of course you are. The rules are simple. The challenger may use substitutions, whereas I may not. The first to run out of able Pokémon to battle loses."

Sierra nods. "Fair enough."

"Let's get started! Pidgey! I choose you!"

The battle goes on for a while, down to each of them having only one Pokémon left.

"You're up, Pidgeotto!" "Pidgeotto!"

Sierra takes a deep breath. "Come on out, Rocky!"

"Excellent choice." He says mildly impressed.

"Thanks." Sierra smiles.

"Pidgeotto! Gust!"

"Rock! Use Rock throw!"

Rocky looks at her with a defiant look, turns to the Pidgeotto and screeches instead. Sierra is in shock at seeing this happen.

"A rather disobedient one you have there." Falkner says with a smirk across his face.

Sierra takes a deep breath. "I must have trained him a little too much...oops. Rocky, could you please use Rock Throw?"

He gives her the same look and uses Screech once again.

Sierra begins to think of a strategy. '_Fine, maybe if I tell him to use Screech, maybe he'll actually use Rock Throw._'

Falkner begins to be rather amused at her willingness to fight on. "Ready to throw in the towel?"

"Not yet! Rocky! Use Screech!"

Falkner looks at her in a surprised manner. "What? Pidgeotto! Watch out!"

Sadly, he does the exact thing Sierra told him to. He uses Screech once again.

Sierra sighs and gets onto her knees. "Please Rocky. I know you're being defiant, and I know why. Just...do this for me...please? I need you. We're both down to our last Pokémon, and down to the last hit points. Okay? I just...I trust you right now."

Rocky gets a contemplative look on his face as he looks at his trainer who is still on her knees. He looks at his opponent, as exhausted as he is and gives a battlecry. Sierra gets back on her feet and gives the command, knocking out Falkner's remaining Pokémon.

The Referee lifts up the flag. "Pidgeotto is unable to battle! The winner is Rocky, and the victory goes to Sierra!"

Falkner smiles after recalling his Pokémon, and Sierra does the same.

"Congratulations, Sierra. I guess I have learned my lesson. Against all odds of a rather rebellious Pokémon, you were still able to beat me. I have a lot to learn from this battle, as do we all when we lose. Well, as proof of defeating me here in Violet City, here is the Zephyr Badge. It will also allow you to use Rock Smash outside of battle, and Pokémon up to level twenty will obey you without question."

"Thank you so much, Falkner."

"Nah. You shouldn't thank me. You should thank your Pokémon." He says with a smile.

"You know? You are absolutely right."

They shake hands and she goes to the Pokémon Center and heals her Pokémon. Afterwards, they celebrate by all of them taking a break from battling the rest of the day.

"All of you were awesome! Thank you so much for your hard work. Especially you, Rocky."

He lets out a loud, happy roar. Sierra smiles. "Alright everyone. Dig in!"

* * *

**(Woohoo! Fifth chapter is finally written out and in the books! I hope you all like it. I really do.)**


End file.
